Depending on how you loaded them. If they are carrier themes loaded with the modified BlackBerry.alx file, then follow the following instructions to update your BlackBerry.alx.
If you downloaded them over-the-air from RIM (such as Smoothie) or from someone on here, then they should appear in Settings > Advanced Options > Applications.
To remove a module that is in use with Javaloader, use the following command:
javaloader -u erase -f <module name>
The -f will flag it to remove an in-use module. If the theme is in-use though, you will likely have a black/white theme once your phone reboots and comes back online.